Abstract

Forkhead box P (FoxP) proteins are unique transcription factors that spatiotemporally regulate gene expression bytethering two chromosome loci togetherviafunctional domain-swapped dimers formed through their DNA-bindingdomains. Further, the differential kinetics on this dimerization mechanism underlie an intricate gene regulationnetwork at physiological conditions. Nonetheless, poor understanding of the structural dynamics and steps of theassociation process impedes to link the functional domain swapping to human-associated diseases. Here, we havecharacterized the DNA-binding domain of human FoxP1 by integrating single-molecule Förster resonance energytransfer and hydrogen–deuterium exchange mass spectrometry data with molecular dynamics simulations. Ourresults confirm the formation of a previously postulated domain-swapped (DS) FoxP1 dimer in solution and revealthe presence of highly populated, heterogeneous, and locally disordered dimeric intermediates along the dimerdissociation pathway. The unique features of FoxP1 provide a glimpse of how intrinsically disordered regions canfacilitate domain swapping oligomerization and other tightly regulated association mechanisms relevant inbiological processes.